readme.renumf90
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readme.renumf90 [2012/05/29 11:50] – ignacio | readme.renumf90 [2012/05/29 12:14] – [Fields in the parameter file] ignacio | ||
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The parameter file contains keywords in capital followed by specifications | The parameter file contains keywords in capital followed by specifications | ||
- | of a given effect/data item. The keywords need to be typed exactly. Specific | + | of a given effect/data item.\\ The keywords need to be typed exactly.\\ Specific |
keywords need to occur sequentially, | keywords need to occur sequentially, | ||
Line 42: | Line 42: | ||
Lines with # are treated as comments | Lines with # are treated as comments | ||
| | ||
- | < | + | < |
DATAFILE | DATAFILE | ||
f1 | f1 | ||
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The data file is f1 | The data file is f1 | ||
- | < | + | < |
TRAITS | TRAITS | ||
t1 t2 .. tn | t1 t2 .. tn | ||
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w is position of weight if present; can be empty | w is position of weight if present; can be empty | ||
- | < | + | < |
RESIDUAL_VARIANCE | RESIDUAL_VARIANCE | ||
r | r | ||
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e1.. en type form | e1.. en type form | ||
</ | </ | ||
- | this line defines one group of effects; e1 .. en are positions of this | + | this line defines one group of effects; e1 .. en are positions of this effect for all traits;\\ |
- | effect for all traits; positions can be different for each trait for fixed | + | positions can be different for each trait for fixed effects;\\ |
- | effects; for random effects, only one position + 0 (misising) efefct are | + | for random effects, only one position + 0 (misising) efefct are |
possible. | possible. | ||
* type is ' | * type is ' | ||
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d1 .. dn form | d1 .. dn form | ||
</ | </ | ||
- | optional for covariables only, specifies nesting; form is as above | + | optional for covariables only, specifies nesting;\\ |
+ | form is as above | ||
| | ||
< | < | ||
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rtype is ' | rtype is ' | ||
- | < | + | < |
OPTIONAL | OPTIONAL | ||
o1 o2.. oq | o1 o2.. oq | ||
</ | </ | ||
- | causes extra effects appended to the animal effect; current options include | + | causes extra effects appended to the animal effect;\\ |
- | ' | + | current options include |
- | permanent environment | + | |
+ | * ' | ||
+ | * 'mpe' for maternal permanent environment | ||
- | < | + | < |
FILE | FILE | ||
fped | fped | ||
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</ | </ | ||
- | for animal effect only; specifies positions in the pedigree file of animal | + | for animal effect only;\\ |
- | an, sire s, dam d, alternate_dam dam rec_dam , and year of birth yob; missing | + | specifies positions in the pedigree file of animal an, sire s, dam d, alternate_dam dam rec_dam , and year of birth yob\\ |
- | alt_dam or yob can be replaced by 0; if this line is not given, defaults are | + | missing alt_dam or yob can be replaced by 0\\ |
- | 1 2 3 0 0. If maternal effect is specified, the maternal effect is due to | + | if this line is not given, defaults are 1 2 3 0 0.\\ |
- | position of d if alt_dam field is 0, or otherwise is due to alt_dam; If | + | If maternal effect is specified, the maternal effect is due to position of d if alt_dam field is 0, or otherwise is due to alt_dam;\\ If alt_dam field is not zero, it should include ID of real or recipient dam. |
- | alt_dam field is not zero, it should include ID of real or recipient | + | |
- | dam. | + | |
- | < | + | < |
SNP_FILE | SNP_FILE | ||
fsnp | fsnp | ||
</ | </ | ||
- | optional; fsnp specifies files with ID and SNP information; | + | optional;\\ |
- | relationship matrix will be constructed as in Aguilar et al. (2010) and will | + | //fsnp// specifies files with ID and SNP information; |
- | include the genomic information; | + | if present, the relationship matrix will be constructed as in Aguilar et al. (2010) and will |
- | same format as fped and SNP info needs to start from a fixed column and | + | include the genomic information; |
- | include digits 0, 1, 2 and 5; ID and SNP info need to be separated by | + | file fsnp should start with ID with the same format as fped and SNP info needs to start from a fixed column and |
- | at leats one space; see info for program PreGSf90 | + | include digits 0, 1, 2 and 5;\\ |
- | < | + | ID and SNP info need to be separated by at leats one space; see info for program |
+ | |||
+ | < | ||
PED_DEPTH | PED_DEPTH | ||
p | p | ||
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the default is 3; all pedigrees are loaded if p=0. | the default is 3; all pedigrees are loaded if p=0. | ||
- | < | + | < |
GEN_INT | GEN_INT | ||
min avg max | min avg max | ||
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pedigree. | pedigree. | ||
- | < | + | < |
REC_SEX | REC_SEX | ||
i | i | ||
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pedigree checks. | pedigree checks. | ||
- | < | + | < |
UPG_TYPE | UPG_TYPE | ||
t | t | ||
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custom_upg(year_of_birth, | custom_upg(year_of_birth, | ||
- | < | + | < |
RANDOM_REGRESSION | RANDOM_REGRESSION | ||
r_type | r_type | ||
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to be generated from a single data variable; not yet implemented | to be generated from a single data variable; not yet implemented | ||
- | < | + | < |
RR_POSITION | RR_POSITION | ||
r1 .. rq | r1 .. rq | ||
Line 195: | Line 198: | ||
</ | </ | ||
- | < | + | < |
(CO)VARIANCES | (CO)VARIANCES | ||
g | g | ||
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account for the maternal effect if present | account for the maternal effect if present | ||
- | < | + | < |
(CO)VARIANCES_PE | (CO)VARIANCES_PE | ||
gpe | gpe | ||
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//gpe// are (co)variances for the PE effect if present | //gpe// are (co)variances for the PE effect if present | ||
- | < | + | < |
(CO)VARIANCES_MPE | (CO)VARIANCES_MPE | ||
gmpe | gmpe | ||
Line 303: | Line 306: | ||
=====Example====== | =====Example====== | ||
+ | |||
+ | |||
+ | **__data file__** - '' | ||
< | < | ||
- | data file - data.test | ||
- | --------------------- | ||
1 aa 34.5 11 12 zz | 1 aa 34.5 11 12 zz | ||
3 bb 21.333 22 23 xx | 3 bb 21.333 22 23 xx | ||
Line 315: | Line 319: | ||
</ | </ | ||
+ | |||
+ | **__pedigree file__** - '' | ||
< | < | ||
- | pedigree file - test.ped | ||
- | ------------------------ | ||
qq 0 0 | qq 0 0 | ||
aa 0 0 | aa 0 0 | ||
Line 325: | Line 329: | ||
</ | </ | ||
- | </ | + | |
- | parameter file - testpar1 | + | **__parameter file__** |
- | ------------------------- | + | < |
# Parameter file for program renf90; it is translated to parameter | # Parameter file for program renf90; it is translated to parameter | ||
# file for BLUPF90 family f programs. | # file for BLUPF90 family f programs. | ||
Line 372: | Line 376: | ||
</ | </ | ||
- | </ | + | **__printout__** \\ |
- | printout | + | \\ |
- | ------------------------------------------------------ | + | (temporary; the amount of details may change) |
+ | < | ||
| | ||
name of parameter file? testpar1 | name of parameter file? testpar1 | ||
Line 465: | Line 470: | ||
</ | </ | ||
+ | **__new parameter file__** - '' | ||
< | < | ||
- | new parameter file - renf90.par | ||
- | ------------------------------- | ||
# BLUPF90 parameter file created by RENF90 | # BLUPF90 parameter file created by RENF90 | ||
DATAFILE | DATAFILE | ||
Line 531: | Line 535: | ||
+ | |||
+ | **__data file__** - '' | ||
< | < | ||
- | data file - renf90.dat | ||
- | ---------------------- | ||
34.5 11 1 3 5 12 1 3 aa 1 | 34.5 11 1 3 5 12 1 3 aa 1 | ||
| | ||
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</ | </ | ||
+ | |||
+ | **__Pedigree file__** - '' | ||
< | < | ||
- | | ||
- | | ||
1 6 3 1 0 2 2 0 0 bb | 1 6 3 1 0 2 2 0 0 bb | ||
6 0 0 1 0 0 0 2 0 qq | 6 0 0 1 0 0 0 2 0 qq | ||
Line 554: | Line 558: | ||
</ | </ | ||
+ | **'' | ||
< | < | ||
- | renumbering tables - renf90.tables | ||
- | ---------------------------------- | ||
| | ||
| |
readme.renumf90.txt · Last modified: 2024/05/22 18:53 by dani